Add option to output all residues involved in each patch #85

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python package

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.8", "3.9", "3.10"]

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v3
	- name: conda environment
	uses: conda-incubator/setup-miniconda@v2
	with:
	mamba-version: "*"
	channels: conda-forge,defaults
	auto-activate-base: true
	- name: Install dependencies
	run: \|
	conda create -y -n my_env python=${{ matrix.python-version }}
	conda activate my_env
	mamba install ambertools mdtraj flake8 pytest -y
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Lint with flake8
	run: \|
	conda activate my_env
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: \|
	conda activate my_env
	python -m pytest

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